Selective amplification of methylated nucleic acids

Chemistry: molecular biology and microbiology – Measuring or testing process involving enzymes or... – Involving nucleic acid

Reexamination Certificate

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C435S091100

Reexamination Certificate

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07989169

ABSTRACT:
The invention is related to a method for amplifying a methylated target nucleic acid in a sample while avoiding amplification of a non-methylated target nucleic acid by inactivating it. This is accomplished by a restriction enzyme digest after bisulfite treatment of the target nucleic acid. The invention is further related to the use of a restriction enzyme to avoid amplification of a non-methylated target nucleic acid while amplifying a methylated target nucleic acid in a sample and kits for performing the methods according to the invention.

REFERENCES:
patent: 4458066 (1984-07-01), Caruthers et al.
patent: 4683202 (1987-07-01), Mullis et al.
patent: 5130238 (1992-07-01), Malek et al.
patent: 5137806 (1992-08-01), LeMaistre et al.
patent: 5210015 (1993-05-01), Gelfand et al.
patent: 5487972 (1996-01-01), Gelfand et al.
patent: 5595890 (1997-01-01), Newton et al.
patent: 5639611 (1997-06-01), Wallace et al.
patent: 5683896 (1997-11-01), Hartley et al.
patent: 5786146 (1998-07-01), Herman et al.
patent: 5804375 (1998-09-01), Gelfand et al.
patent: 6004826 (1999-12-01), Segev
patent: 6174670 (2001-01-01), Wittwer et al.
patent: 6180344 (2001-01-01), Chen
patent: 6331393 (2001-12-01), Laird et al.
patent: 2003/0082600 (2003-05-01), Olek et al.
patent: 2004/0146868 (2004-07-01), Cottrell et al.
patent: 2005/0069879 (2005-03-01), Berlin
patent: 0 200 362 (1986-12-01), None
patent: 0 201 184 (1986-12-01), None
patent: 0 389 063 (1990-09-01), None
patent: 0 401 037 (1990-12-01), None
patent: 0 439 182 (1991-07-01), None
patent: 0 415 755 (1995-12-01), None
patent: 0 976 835 (2000-02-01), None
patent: 1 394 173 (2004-03-01), None
patent: 04020974.4 (2005-01-01), None
patent: WO 90/01069 (1990-02-01), None
patent: WO 92/02638 (1992-02-01), None
patent: WO 92/08808 (1992-05-01), None
patent: WO 01/37291 (2001-05-01), None
patent: WO 01/37291 (2001-05-01), None
patent: WO 02/061124 (2002-08-01), None
patent: WO 03/027259 (2003-04-01), None
patent: WO 03/027259 (2003-04-01), None
patent: WO 03/064701 (2003-08-01), None
patent: WO 03/064701 (2003-08-01), None
patent: WO 2004/067777 (2004-08-01), None
patent: WO 2006/009870 (2006-01-01), None
patent: WO 2006/009870 (2006-01-01), None
patent: WO 2005/009475 (2006-03-01), None
patent: WO 2006/024541 (2006-03-01), None
Kornberg, Minireview DNA Replication, The Journal of Biological Chemistry, vol. 263, No. 1, Issue of Jan. 5, pp. 1-4, 1988.
Ghoshal et al., Inhibitors of Histone Deacetylase and DNA Methyltransferase Synergistically Activate the Methylated Metallothionein I Promoter by Activating the Transcription Factor MTF-1 and Forming an Open Chromatin Structure, Molecular and Cellular Biology, Dec. 2002, p. 8302-8319 vol. 22, No. 23.
Rein et al., Survey and Summary Identifying 5-methylcytosine and related modifications in DNA genomes,Nucleic Acids Research, 1998, vol. 26, No. 10 2255-2264.
Klein et al., Comparative genomic hybridization, loss of heterozygosity, and DNA sequence analysis of single cells, Proc. Natl. Acad. Sci. USA, vol. 96, pp. 4494-4499, Apr. 1999.
Sadri et al., Rapid analysis of DNA methylation using new restriction enzyme sites created by bisulfite modification, Nucleic Acids Research, 1996, vol. 24, No. 24, pp. 5058-5059.
Abramson, R., et al, 1993, “Nucleic acid amplification technologies”,Current Opinion in Biotechnology, 4: 41-47.
Abravaya, K., et al, 2005, “Strategies to Avoid Amplicon Contamination”,Abbott Laboratories, 125-133.
Ausubel, F., et al., 2001, Current Protocols in Molecular Biology, vol. 1.
Ausubel, F., et al., 2001, Current Protocols in Molecular Biology, vol. 2.
Ausubel, F., et al., 2001, Current Protocols in Molecular Biology, vol. 3.
Barany, F., et al, 1991, “Genetic disease detection and DNA amplification using cloned thermostable ligase”,Proc. Natl. Acad. Sci. USA, 88 189-193.
Barany, F., et al, 1991, “Review: The Ligase Chain Reaction in a PCR World”,PCR Methods and Applications, 1: 5-16.
Beaucage, S., et al, 1981, “Deoxynucleoside Phosphoramidities—A New Class of Key Intermediates for Deoxypolynucleotide Synthesis”,Tetrahedron Letters, 22 (20): 1859-1862.
Benyajati, C., et al, 1980, “Alcohol dehydrogenase inDrosophila: isolation and characterization of messenger RNA and cDNA clone”,Nucleic Acids Research, 8 (23) 5649-5667.
Brown, E., et al, 1979, “Chemical Synthesis and Cloning of a Tyrosine tRNA Gene”,Methods in Enzymology, 68 109-151.
Cedar, H., et al, 1979, “Direct detection of methylated cytosine in DNA by use of the restriction enzyme Mspl”,Nucleic Acids Research, 6 (6): 2125-2132.
Chang, S., et al, 1992, “PCR Amplification Following Restriction to Detect Site-Specific DNA Methylation”,Plant Molecular Biology Reporter, 10 (4) 362-366.
Clark, S., et al, 1994, “High Sensitivity Mapping of Methylated Cytosines”,Nucleic Acids Research, 22 (15) 2990-2997.
Clark, S., et al, 1997, “Bisulphite Genomic Sequencing of Methylated Cytosines”, Detection of Mutations and Polymorphisms in DNA, Chapter 14, pp. 151-162, CRC Press, Inc.
Feil, R., et al, 1994, “Methylation analysis on individual chromosomes: improved protocol for bisulphate genomic sequencing”,Nucleic Acids Research, 22 (4): 695-696.
Fojtová, M., et al, 2001, “Cytosine methylation of plastid genome in higher plants, Fact or artifact?”,Plant Science, 160 585-593.
Frommer, M., et al, 1992, “A genomic sequencing protocol that yields a positive display of 5-methylcytosine residues in individual DNA strands”,Proc. Natl. Acad. Sci. USA, 89: 1827-1831.
Gait, M., 1984, “Oligonucleotide Synthesis, A Practical Approach”, ISBN 0-904147-74-6, IRL Press, Oxford, England.
Garegg, P., et al, 1985, “Formation of Internucleotidic bonds via Phosphonate Intermediates”,Chemica Scripta, 25: 280-282.
Grigg, G., 1994, “Sequencing 5-Methylcytosine Residues in Genomic DNA”,BioEssays, 16 (6): 431-436.
Grigg, G., 1996, “Sequencing 5-methylcytosine residues by the bisulphate method”,DNA Sequence—The Journal of Sequencing and Mapping, 6: 189-198.
Grunau, C., 2001, “Bisulfite genomic sequencing: systematic investigation of critical experimental parameters”,Nucleic Acids Research, 29 (13 e65): 1-7.
Guatelli, J., et al, 1990, “Isothermal, in vitro amplification of nucleic acids by a multienzyme reaction modeled after retroviral replication”,Proc. Natl. Acad. Sci. USA, 87: 1874-1878.
Ki-Hyo, J., et al, 2001, “Identification of a Sequence Containing Methylated Cytidine inCorynebacterium glutamicumandBrevibacterium flavumUsing Bisulfite DNA Derivatization and Sequencing”,J. Microbiol. Biotechnol, 11 (5): 819-824.
Klaschik, S., et al, 2002, “Comparison of Different Decontamination Methods for Reagents to Detect Low Concentrations of Bacterial 16S DNA by Real-Time-PCR”,Molecular Biotechnology, 22: 231-242.
Komiyama, M., et al, 1994, “Catalysis of Diethylenetriamine for Bisulfite-Induced Deamination of Cytosine in Oligodeoxyribonucleotides”,Tetrahedron Letters, 35 (44): 8185-8188.
Kupper, D., et al, 1997, “Reliable Detection of DNA GpG Methylation Profiles by the Isoschizomers MspI/HpaII Using Oligonucleotide Stimulators”,Biotechniques, 23 (5): 843-846.
Kwoh, D., et al, 1989, “Transcription-based amplification system and detection of amplified human immunodeficiency virus type 1 with a bead-based sandwich hybridization format”,Proc. Natl. Acad. Sci. USA, 86: 1173-1177.
Narang, S., et al, 1979, “Improved Phosphotriester method for the Synthesis of Gene Fragments”,Methods in Enzymology, 68: 90-98.
Oakeley, E., 1999, “DNA methylation analysis: a review of current methodologies”,Phamacology&Therapeutics, 84: 389-400.
Olek, A., et al, 1996, “A medofied and improved method for bisulphate based cytosine methylatiohn analysis”,Nucleic Acids Research, 24 (24): 5064-5066.
Paulin, R.,

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